Starting phenix.real_space_refine on Thu Jan 23 13:40:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xfe_38302/01_2025/8xfe_38302.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xfe_38302/01_2025/8xfe_38302.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xfe_38302/01_2025/8xfe_38302.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xfe_38302/01_2025/8xfe_38302.map" model { file = "/net/cci-nas-00/data/ceres_data/8xfe_38302/01_2025/8xfe_38302.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xfe_38302/01_2025/8xfe_38302.cif" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 13269 2.51 5 N 3323 2.21 5 O 3675 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 53 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 20339 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 981, 7738 Classifications: {'peptide': 981} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 109} Link IDs: {'PTRANS': 19, 'TRANS': 961} Unresolved non-hydrogen bonds: 435 Unresolved non-hydrogen angles: 521 Unresolved non-hydrogen dihedrals: 362 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 5, 'ASP:plan': 18, 'PHE:plan': 4, 'GLU:plan': 36, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 299 Chain: "B" Number of atoms: 7529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 984, 7529 Classifications: {'peptide': 984} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 176} Link IDs: {'PTRANS': 19, 'TRANS': 964} Unresolved non-hydrogen bonds: 667 Unresolved non-hydrogen angles: 801 Unresolved non-hydrogen dihedrals: 543 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 1, 'ASN:plan1': 19, 'ASP:plan': 27, 'PHE:plan': 4, 'GLU:plan': 54, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 451 Chain: "C" Number of atoms: 894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 894 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 111} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 25 Chain: "D" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2129 Classifications: {'peptide': 273} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 10, 'TRANS': 262} Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 9, 'ASN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 70 Chain: "E" Number of atoms: 2049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2049 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 10, 'TRANS': 261} Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 210 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 12, 'ARG:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 13} Unresolved non-hydrogen planarities: 123 Time building chain proxies: 14.12, per 1000 atoms: 0.69 Number of scatterers: 20339 At special positions: 0 Unit cell: (100.1, 128.7, 183.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 3675 8.00 N 3323 7.00 C 13269 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.44 Conformation dependent library (CDL) restraints added in 3.0 seconds 5230 Ramachandran restraints generated. 2615 Oldfield, 0 Emsley, 2615 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4992 Finding SS restraints... Secondary structure from input PDB file: 146 helices and 9 sheets defined 57.2% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.30 Creating SS restraints... Processing helix chain 'A' and resid 25 through 38 removed outlier: 4.087A pdb=" N CYS A 29 " --> pdb=" O ASN A 25 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER A 36 " --> pdb=" O GLU A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 71 removed outlier: 3.705A pdb=" N LEU A 62 " --> pdb=" O GLN A 58 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS A 65 " --> pdb=" O ARG A 61 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU A 68 " --> pdb=" O ASP A 64 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU A 70 " --> pdb=" O TYR A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 96 removed outlier: 3.912A pdb=" N ARG A 86 " --> pdb=" O ASP A 82 " (cutoff:3.500A) Proline residue: A 88 - end of helix removed outlier: 3.703A pdb=" N GLY A 96 " --> pdb=" O TYR A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 108 removed outlier: 3.793A pdb=" N PHE A 100 " --> pdb=" O GLY A 96 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU A 104 " --> pdb=" O PHE A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 123 removed outlier: 3.789A pdb=" N ASP A 119 " --> pdb=" O ASN A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 144 removed outlier: 3.504A pdb=" N LYS A 144 " --> pdb=" O THR A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 159 removed outlier: 3.825A pdb=" N VAL A 158 " --> pdb=" O GLU A 155 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA A 159 " --> pdb=" O GLU A 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 155 through 159' Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 197 through 211 removed outlier: 3.821A pdb=" N SER A 201 " --> pdb=" O TYR A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 234 removed outlier: 3.865A pdb=" N TRP A 231 " --> pdb=" O MET A 227 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS A 234 " --> pdb=" O ASN A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 263 Processing helix chain 'A' and resid 282 through 298 removed outlier: 3.737A pdb=" N VAL A 289 " --> pdb=" O ARG A 285 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A 292 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER A 296 " --> pdb=" O LEU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 317 Processing helix chain 'A' and resid 318 through 322 removed outlier: 3.571A pdb=" N LEU A 322 " --> pdb=" O LEU A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 334 Processing helix chain 'A' and resid 355 through 366 removed outlier: 3.680A pdb=" N PHE A 361 " --> pdb=" O MET A 357 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU A 362 " --> pdb=" O GLU A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 391 removed outlier: 3.901A pdb=" N GLU A 379 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N PHE A 381 " --> pdb=" O GLN A 377 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 384 " --> pdb=" O ARG A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 416 removed outlier: 3.503A pdb=" N HIS A 415 " --> pdb=" O SER A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 426 Processing helix chain 'A' and resid 433 through 445 removed outlier: 3.513A pdb=" N PHE A 440 " --> pdb=" O TYR A 436 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA A 443 " --> pdb=" O ALA A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 462 removed outlier: 3.577A pdb=" N LEU A 460 " --> pdb=" O SER A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 496 removed outlier: 3.557A pdb=" N TYR A 479 " --> pdb=" O GLN A 475 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR A 490 " --> pdb=" O THR A 486 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN A 491 " --> pdb=" O GLN A 487 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASN A 493 " --> pdb=" O VAL A 489 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU A 495 " --> pdb=" O GLN A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 519 removed outlier: 3.988A pdb=" N ARG A 514 " --> pdb=" O GLU A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 531 removed outlier: 3.509A pdb=" N LEU A 527 " --> pdb=" O ILE A 524 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N PHE A 528 " --> pdb=" O ASP A 525 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN A 529 " --> pdb=" O ASP A 526 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N MET A 531 " --> pdb=" O PHE A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 539 Processing helix chain 'A' and resid 542 through 547 removed outlier: 3.663A pdb=" N LEU A 545 " --> pdb=" O LEU A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 557 removed outlier: 3.632A pdb=" N THR A 555 " --> pdb=" O LEU A 551 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL A 556 " --> pdb=" O TYR A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 563 removed outlier: 3.971A pdb=" N THR A 562 " --> pdb=" O LEU A 558 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ASN A 563 " --> pdb=" O PHE A 559 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 558 through 563' Processing helix chain 'A' and resid 564 through 572 removed outlier: 4.345A pdb=" N SER A 570 " --> pdb=" O ARG A 566 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLU A 571 " --> pdb=" O SER A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 598 removed outlier: 3.637A pdb=" N VAL A 584 " --> pdb=" O SER A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 604 removed outlier: 3.576A pdb=" N VAL A 603 " --> pdb=" O LEU A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 633 removed outlier: 3.802A pdb=" N LEU A 618 " --> pdb=" O ASN A 614 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS A 622 " --> pdb=" O LEU A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 659 removed outlier: 3.553A pdb=" N HIS A 658 " --> pdb=" O ASN A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 670 removed outlier: 3.684A pdb=" N ASN A 666 " --> pdb=" O ASP A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 676 Processing helix chain 'A' and resid 680 through 689 removed outlier: 3.739A pdb=" N GLU A 686 " --> pdb=" O GLU A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 700 Processing helix chain 'A' and resid 706 through 722 removed outlier: 3.645A pdb=" N THR A 710 " --> pdb=" O VAL A 706 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN A 711 " --> pdb=" O VAL A 707 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N SER A 714 " --> pdb=" O THR A 710 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLU A 715 " --> pdb=" O GLN A 711 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 720 " --> pdb=" O ALA A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 726 Processing helix chain 'A' and resid 729 through 742 removed outlier: 3.516A pdb=" N GLY A 734 " --> pdb=" O GLU A 730 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LYS A 735 " --> pdb=" O GLU A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 761 removed outlier: 3.579A pdb=" N TYR A 755 " --> pdb=" O ILE A 751 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU A 761 " --> pdb=" O TRP A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 776 removed outlier: 3.663A pdb=" N ILE A 775 " --> pdb=" O ILE A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 784 removed outlier: 3.556A pdb=" N LEU A 781 " --> pdb=" O ASP A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 810 removed outlier: 3.898A pdb=" N TYR A 804 " --> pdb=" O TYR A 800 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY A 805 " --> pdb=" O SER A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 839 removed outlier: 3.648A pdb=" N ASP A 836 " --> pdb=" O GLN A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 840 through 845 Proline residue: A 843 - end of helix No H-bonds generated for 'chain 'A' and resid 840 through 845' Processing helix chain 'A' and resid 846 through 854 removed outlier: 3.631A pdb=" N HIS A 852 " --> pdb=" O ASN A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 857 No H-bonds generated for 'chain 'A' and resid 855 through 857' Processing helix chain 'A' and resid 861 through 871 removed outlier: 4.011A pdb=" N ASN A 867 " --> pdb=" O ASN A 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 902 removed outlier: 4.153A pdb=" N LEU A 884 " --> pdb=" O GLU A 880 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE A 885 " --> pdb=" O HIS A 881 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE A 897 " --> pdb=" O LYS A 893 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N VAL A 898 " --> pdb=" O VAL A 894 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU A 901 " --> pdb=" O ILE A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 922 removed outlier: 3.518A pdb=" N GLY A 917 " --> pdb=" O MET A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 930 through 934 removed outlier: 3.531A pdb=" N ILE A 934 " --> pdb=" O GLU A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 945 removed outlier: 3.553A pdb=" N ASP A 945 " --> pdb=" O ASP A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 950 through 954 Processing helix chain 'A' and resid 955 through 961 Processing helix chain 'A' and resid 963 through 971 removed outlier: 3.583A pdb=" N GLY A 968 " --> pdb=" O ASP A 964 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS A 969 " --> pdb=" O LYS A 965 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 989 removed outlier: 3.501A pdb=" N VAL A 980 " --> pdb=" O MET A 976 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU A 982 " --> pdb=" O HIS A 978 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG A 987 " --> pdb=" O VAL A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 1003 Processing helix chain 'B' and resid 24 through 38 removed outlier: 3.948A pdb=" N GLU B 35 " --> pdb=" O LYS B 31 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG B 38 " --> pdb=" O THR B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 52 removed outlier: 4.170A pdb=" N SER B 51 " --> pdb=" O GLY B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 64 removed outlier: 3.543A pdb=" N VAL B 63 " --> pdb=" O TRP B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 69 Processing helix chain 'B' and resid 81 through 86 removed outlier: 3.851A pdb=" N ARG B 86 " --> pdb=" O ASP B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 94 Processing helix chain 'B' and resid 99 through 108 removed outlier: 3.886A pdb=" N ILE B 103 " --> pdb=" O ALA B 99 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU B 104 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LYS B 105 " --> pdb=" O ASP B 101 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP B 106 " --> pdb=" O GLY B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 123 removed outlier: 3.948A pdb=" N ASP B 119 " --> pdb=" O ASN B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 145 removed outlier: 3.803A pdb=" N ARG B 145 " --> pdb=" O ALA B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 158 removed outlier: 3.733A pdb=" N ASP B 157 " --> pdb=" O ALA B 154 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL B 158 " --> pdb=" O GLU B 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 154 through 158' Processing helix chain 'B' and resid 192 through 197 Processing helix chain 'B' and resid 199 through 211 Processing helix chain 'B' and resid 222 through 230 Processing helix chain 'B' and resid 254 through 263 Processing helix chain 'B' and resid 272 through 274 No H-bonds generated for 'chain 'B' and resid 272 through 274' Processing helix chain 'B' and resid 281 through 296 removed outlier: 4.341A pdb=" N ARG B 285 " --> pdb=" O ASP B 281 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL B 289 " --> pdb=" O ARG B 285 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE B 294 " --> pdb=" O MET B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 317 removed outlier: 3.716A pdb=" N ILE B 309 " --> pdb=" O ASP B 305 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASP B 310 " --> pdb=" O ASP B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 321 Processing helix chain 'B' and resid 329 through 334 Processing helix chain 'B' and resid 357 through 366 removed outlier: 3.578A pdb=" N SER B 366 " --> pdb=" O GLU B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 379 removed outlier: 3.787A pdb=" N GLU B 379 " --> pdb=" O LYS B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 392 Processing helix chain 'B' and resid 411 through 416 removed outlier: 3.520A pdb=" N HIS B 415 " --> pdb=" O SER B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 426 removed outlier: 3.537A pdb=" N MET B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS B 423 " --> pdb=" O ASP B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 445 removed outlier: 3.709A pdb=" N LYS B 438 " --> pdb=" O ASP B 434 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE B 440 " --> pdb=" O TYR B 436 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N PHE B 441 " --> pdb=" O LYS B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 462 removed outlier: 3.623A pdb=" N ASP B 453 " --> pdb=" O GLU B 449 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE B 458 " --> pdb=" O LEU B 454 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU B 460 " --> pdb=" O SER B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 466 Processing helix chain 'B' and resid 468 through 488 removed outlier: 3.532A pdb=" N THR B 486 " --> pdb=" O TYR B 482 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN B 487 " --> pdb=" O GLN B 483 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA B 488 " --> pdb=" O SER B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 519 removed outlier: 3.706A pdb=" N GLU B 516 " --> pdb=" O LEU B 512 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG B 517 " --> pdb=" O ALA B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 527 removed outlier: 3.664A pdb=" N LEU B 527 " --> pdb=" O ILE B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 547 removed outlier: 3.951A pdb=" N GLU B 543 " --> pdb=" O LYS B 540 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N PHE B 544 " --> pdb=" O ILE B 541 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER B 546 " --> pdb=" O GLU B 543 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP B 547 " --> pdb=" O PHE B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 570 removed outlier: 3.567A pdb=" N LYS B 557 " --> pdb=" O ASP B 553 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASN B 563 " --> pdb=" O PHE B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 596 removed outlier: 3.689A pdb=" N ASN B 591 " --> pdb=" O ARG B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 604 removed outlier: 3.551A pdb=" N VAL B 603 " --> pdb=" O LEU B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 628 removed outlier: 3.657A pdb=" N HIS B 609 " --> pdb=" O PHE B 605 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU B 618 " --> pdb=" O ASN B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 659 removed outlier: 3.590A pdb=" N PHE B 652 " --> pdb=" O GLU B 648 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N HIS B 658 " --> pdb=" O ASN B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 671 Processing helix chain 'B' and resid 672 through 676 Processing helix chain 'B' and resid 681 through 695 removed outlier: 4.251A pdb=" N GLU B 686 " --> pdb=" O GLU B 682 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N TYR B 687 " --> pdb=" O LYS B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 722 removed outlier: 4.202A pdb=" N GLN B 711 " --> pdb=" O VAL B 707 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N SER B 714 " --> pdb=" O THR B 710 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU B 715 " --> pdb=" O GLN B 711 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA B 718 " --> pdb=" O SER B 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 725 No H-bonds generated for 'chain 'B' and resid 723 through 725' Processing helix chain 'B' and resid 729 through 742 removed outlier: 4.347A pdb=" N LYS B 735 " --> pdb=" O GLU B 731 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE B 742 " --> pdb=" O LYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 751 through 760 removed outlier: 4.119A pdb=" N TRP B 757 " --> pdb=" O LYS B 753 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU B 758 " --> pdb=" O ARG B 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 786 removed outlier: 3.616A pdb=" N ILE B 772 " --> pdb=" O PRO B 768 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER B 773 " --> pdb=" O LYS B 769 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ILE B 774 " --> pdb=" O SER B 770 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU B 781 " --> pdb=" O ASP B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 802 through 812 removed outlier: 3.731A pdb=" N PHE B 811 " --> pdb=" O LEU B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 831 through 841 removed outlier: 3.547A pdb=" N PHE B 837 " --> pdb=" O LYS B 833 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU B 841 " --> pdb=" O PHE B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 842 through 845 Processing helix chain 'B' and resid 846 through 855 removed outlier: 4.110A pdb=" N SER B 851 " --> pdb=" O THR B 847 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N HIS B 852 " --> pdb=" O ASN B 848 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU B 853 " --> pdb=" O ALA B 849 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 871 removed outlier: 3.582A pdb=" N ASN B 867 " --> pdb=" O ASN B 863 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ARG B 870 " --> pdb=" O MET B 866 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE B 871 " --> pdb=" O ASN B 867 " (cutoff:3.500A) Processing helix chain 'B' and resid 878 through 903 removed outlier: 3.568A pdb=" N GLU B 882 " --> pdb=" O THR B 878 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU B 883 " --> pdb=" O PRO B 879 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU B 884 " --> pdb=" O GLU B 880 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS B 900 " --> pdb=" O TYR B 896 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLU B 901 " --> pdb=" O ILE B 897 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS B 902 " --> pdb=" O VAL B 898 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 922 removed outlier: 3.537A pdb=" N PHE B 916 " --> pdb=" O TYR B 912 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY B 917 " --> pdb=" O MET B 913 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE B 918 " --> pdb=" O SER B 914 " (cutoff:3.500A) Processing helix chain 'B' and resid 929 through 934 removed outlier: 3.782A pdb=" N GLU B 932 " --> pdb=" O LYS B 929 " (cutoff:3.500A) Processing helix chain 'B' and resid 937 through 945 removed outlier: 3.663A pdb=" N PHE B 943 " --> pdb=" O GLN B 939 " (cutoff:3.500A) Processing helix chain 'B' and resid 950 through 954 removed outlier: 4.085A pdb=" N PHE B 954 " --> pdb=" O TYR B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 955 through 962 removed outlier: 3.674A pdb=" N LYS B 960 " --> pdb=" O SER B 957 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TYR B 962 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 963 through 971 Processing helix chain 'B' and resid 973 through 978 removed outlier: 4.729A pdb=" N HIS B 978 " --> pdb=" O LYS B 974 " (cutoff:3.500A) Processing helix chain 'B' and resid 981 through 990 removed outlier: 3.511A pdb=" N GLU B 986 " --> pdb=" O GLU B 982 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG B 987 " --> pdb=" O VAL B 983 " (cutoff:3.500A) Processing helix chain 'B' and resid 994 through 1004 removed outlier: 3.630A pdb=" N GLU B 998 " --> pdb=" O LYS B 994 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 102 Processing helix chain 'D' and resid 26 through 39 removed outlier: 3.511A pdb=" N GLU D 32 " --> pdb=" O GLU D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 53 removed outlier: 3.625A pdb=" N LEU D 53 " --> pdb=" O GLY D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 69 removed outlier: 3.852A pdb=" N LEU D 62 " --> pdb=" O GLN D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 96 Processing helix chain 'D' and resid 100 through 109 removed outlier: 3.597A pdb=" N LEU D 104 " --> pdb=" O PHE D 100 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASP D 106 " --> pdb=" O GLY D 102 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 121 Processing helix chain 'D' and resid 122 through 125 removed outlier: 3.600A pdb=" N ASN D 125 " --> pdb=" O LEU D 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 122 through 125' Processing helix chain 'D' and resid 139 through 145 removed outlier: 3.535A pdb=" N TRP D 143 " --> pdb=" O ASP D 139 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG D 145 " --> pdb=" O ALA D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 159 removed outlier: 3.565A pdb=" N ASP D 157 " --> pdb=" O ALA D 154 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL D 158 " --> pdb=" O GLU D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 191 Processing helix chain 'D' and resid 192 through 197 Processing helix chain 'D' and resid 197 through 211 removed outlier: 3.568A pdb=" N SER D 201 " --> pdb=" O TYR D 197 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS D 205 " --> pdb=" O SER D 201 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE D 207 " --> pdb=" O LEU D 203 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA D 209 " --> pdb=" O LYS D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 235 removed outlier: 3.817A pdb=" N ASN D 226 " --> pdb=" O ASP D 222 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N MET D 227 " --> pdb=" O TYR D 223 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU D 228 " --> pdb=" O ASN D 224 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS D 234 " --> pdb=" O ASN D 230 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU D 235 " --> pdb=" O TRP D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 264 Processing helix chain 'D' and resid 271 through 275 Processing helix chain 'D' and resid 281 through 295 removed outlier: 3.700A pdb=" N ARG D 285 " --> pdb=" O ASP D 281 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N VAL D 289 " --> pdb=" O ARG D 285 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N MET D 290 " --> pdb=" O TYR D 286 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU D 293 " --> pdb=" O VAL D 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 40 removed outlier: 3.853A pdb=" N ILE E 33 " --> pdb=" O CYS E 29 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N THR E 34 " --> pdb=" O ILE E 30 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG E 38 " --> pdb=" O THR E 34 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASN E 39 " --> pdb=" O GLU E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 71 removed outlier: 3.575A pdb=" N LEU E 70 " --> pdb=" O TYR E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 94 removed outlier: 3.838A pdb=" N ASN E 93 " --> pdb=" O GLN E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 109 removed outlier: 3.980A pdb=" N ASP E 101 " --> pdb=" O GLU E 97 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE E 103 " --> pdb=" O ALA E 99 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU E 104 " --> pdb=" O PHE E 100 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP E 106 " --> pdb=" O GLY E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 123 removed outlier: 3.585A pdb=" N ASP E 119 " --> pdb=" O ASN E 115 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU E 122 " --> pdb=" O HIS E 118 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA E 123 " --> pdb=" O ASP E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 177 removed outlier: 4.450A pdb=" N LYS E 176 " --> pdb=" O ASP E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 183 removed outlier: 3.828A pdb=" N ASN E 182 " --> pdb=" O LYS E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 192 through 197 Processing helix chain 'E' and resid 197 through 211 removed outlier: 3.706A pdb=" N SER E 201 " --> pdb=" O TYR E 197 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LYS E 205 " --> pdb=" O SER E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 233 removed outlier: 4.328A pdb=" N ASN E 226 " --> pdb=" O ASP E 222 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU E 228 " --> pdb=" O ASN E 224 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU E 229 " --> pdb=" O ILE E 225 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TRP E 231 " --> pdb=" O MET E 227 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG E 233 " --> pdb=" O LEU E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 262 removed outlier: 3.647A pdb=" N LEU E 258 " --> pdb=" O GLU E 254 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE E 259 " --> pdb=" O ASN E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 295 removed outlier: 3.821A pdb=" N ALA E 288 " --> pdb=" O GLU E 284 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL E 289 " --> pdb=" O ARG E 285 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N MET E 290 " --> pdb=" O TYR E 286 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 150 through 152 removed outlier: 6.143A pdb=" N SER A 150 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LYS A 169 " --> pdb=" O SER A 150 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE A 152 " --> pdb=" O LYS A 169 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N HIS A 128 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE A 44 " --> pdb=" O HIS A 128 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ILE A 213 " --> pdb=" O PHE A 244 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N ILE A 246 " --> pdb=" O ILE A 213 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N PHE A 215 " --> pdb=" O ILE A 246 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 338 through 340 Processing sheet with id=AA3, first strand: chain 'B' and resid 150 through 152 removed outlier: 6.804A pdb=" N LEU B 42 " --> pdb=" O HIS B 128 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N ILE B 130 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N PHE B 44 " --> pdb=" O ILE B 130 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ILE B 213 " --> pdb=" O PHE B 244 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ILE B 246 " --> pdb=" O ILE B 213 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N PHE B 215 " --> pdb=" O ILE B 246 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N PHE B 245 " --> pdb=" O ILE B 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 338 through 340 Processing sheet with id=AA5, first strand: chain 'B' and resid 573 through 575 removed outlier: 6.720A pdb=" N PHE C 23 " --> pdb=" O VAL C 113 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 27 through 32 removed outlier: 6.778A pdb=" N VAL C 32 " --> pdb=" O ILE C 83 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N ILE C 83 " --> pdb=" O VAL C 32 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 62 through 67 removed outlier: 4.054A pdb=" N GLU C 115 " --> pdb=" O PHE C 44 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 150 through 152 removed outlier: 6.989A pdb=" N ILE D 213 " --> pdb=" O PHE D 244 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N ILE D 246 " --> pdb=" O ILE D 213 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N PHE D 215 " --> pdb=" O ILE D 246 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 150 through 152 removed outlier: 6.014A pdb=" N VAL E 129 " --> pdb=" O LEU E 168 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LEU E 42 " --> pdb=" O HIS E 128 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N ILE E 130 " --> pdb=" O LEU E 42 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N PHE E 44 " --> pdb=" O ILE E 130 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ILE E 246 " --> pdb=" O PHE E 215 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE E 269 " --> pdb=" O PHE E 245 " (cutoff:3.500A) 788 hydrogen bonds defined for protein. 2244 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.38 Time building geometry restraints manager: 5.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4519 1.33 - 1.45: 5061 1.45 - 1.57: 11142 1.57 - 1.69: 0 1.69 - 1.81: 117 Bond restraints: 20839 Sorted by residual: bond pdb=" C ILE E 87 " pdb=" N PRO E 88 " ideal model delta sigma weight residual 1.336 1.396 -0.060 1.23e-02 6.61e+03 2.41e+01 bond pdb=" N ILE B 253 " pdb=" CA ILE B 253 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.32e-02 5.74e+03 7.48e+00 bond pdb=" C TYR E 56 " pdb=" N PRO E 57 " ideal model delta sigma weight residual 1.331 1.362 -0.031 1.20e-02 6.94e+03 6.62e+00 bond pdb=" N SER A 575 " pdb=" CA SER A 575 " ideal model delta sigma weight residual 1.456 1.488 -0.031 1.23e-02 6.61e+03 6.49e+00 bond pdb=" N SER A 579 " pdb=" CA SER A 579 " ideal model delta sigma weight residual 1.453 1.486 -0.033 1.37e-02 5.33e+03 5.70e+00 ... (remaining 20834 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 26993 2.08 - 4.16: 1126 4.16 - 6.24: 158 6.24 - 8.32: 35 8.32 - 10.39: 11 Bond angle restraints: 28323 Sorted by residual: angle pdb=" N ILE A 309 " pdb=" CA ILE A 309 " pdb=" C ILE A 309 " ideal model delta sigma weight residual 111.91 106.21 5.70 8.90e-01 1.26e+00 4.09e+01 angle pdb=" C LYS A 75 " pdb=" N LYS A 76 " pdb=" CA LYS A 76 " ideal model delta sigma weight residual 120.79 127.07 -6.28 1.39e+00 5.18e-01 2.04e+01 angle pdb=" C PHE A 576 " pdb=" CA PHE A 576 " pdb=" CB PHE A 576 " ideal model delta sigma weight residual 116.54 111.43 5.11 1.15e+00 7.56e-01 1.97e+01 angle pdb=" N ILE D 138 " pdb=" CA ILE D 138 " pdb=" C ILE D 138 " ideal model delta sigma weight residual 113.07 107.01 6.06 1.37e+00 5.33e-01 1.96e+01 angle pdb=" N ILE B 138 " pdb=" CA ILE B 138 " pdb=" C ILE B 138 " ideal model delta sigma weight residual 112.50 106.92 5.58 1.39e+00 5.18e-01 1.61e+01 ... (remaining 28318 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.52: 11521 16.52 - 33.04: 520 33.04 - 49.56: 96 49.56 - 66.08: 9 66.08 - 82.60: 6 Dihedral angle restraints: 12152 sinusoidal: 4373 harmonic: 7779 Sorted by residual: dihedral pdb=" CA ASN B 78 " pdb=" C ASN B 78 " pdb=" N TYR B 79 " pdb=" CA TYR B 79 " ideal model delta harmonic sigma weight residual -180.00 -150.84 -29.16 0 5.00e+00 4.00e-02 3.40e+01 dihedral pdb=" CA PHE A 699 " pdb=" C PHE A 699 " pdb=" N SER A 700 " pdb=" CA SER A 700 " ideal model delta harmonic sigma weight residual 180.00 152.31 27.69 0 5.00e+00 4.00e-02 3.07e+01 dihedral pdb=" CA GLU B 766 " pdb=" C GLU B 766 " pdb=" N LEU B 767 " pdb=" CA LEU B 767 " ideal model delta harmonic sigma weight residual 180.00 -152.95 -27.05 0 5.00e+00 4.00e-02 2.93e+01 ... (remaining 12149 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2254 0.060 - 0.119: 799 0.119 - 0.179: 116 0.179 - 0.238: 10 0.238 - 0.298: 4 Chirality restraints: 3183 Sorted by residual: chirality pdb=" CB ILE B 736 " pdb=" CA ILE B 736 " pdb=" CG1 ILE B 736 " pdb=" CG2 ILE B 736 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CB ILE A 407 " pdb=" CA ILE A 407 " pdb=" CG1 ILE A 407 " pdb=" CG2 ILE A 407 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" CA GLU B 680 " pdb=" N GLU B 680 " pdb=" C GLU B 680 " pdb=" CB GLU B 680 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.69e+00 ... (remaining 3180 not shown) Planarity restraints: 3580 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 25 " 0.037 2.00e-02 2.50e+03 2.80e-02 1.96e+01 pdb=" CG TRP C 25 " -0.077 2.00e-02 2.50e+03 pdb=" CD1 TRP C 25 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP C 25 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 25 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 25 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP C 25 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 25 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 25 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C 25 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 678 " 0.014 2.00e-02 2.50e+03 2.17e-02 8.26e+00 pdb=" CG PHE B 678 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 PHE B 678 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 PHE B 678 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE B 678 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 PHE B 678 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE B 678 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 559 " 0.020 2.00e-02 2.50e+03 2.16e-02 8.19e+00 pdb=" CG PHE A 559 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 PHE A 559 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE A 559 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A 559 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 559 " 0.012 2.00e-02 2.50e+03 pdb=" CZ PHE A 559 " -0.002 2.00e-02 2.50e+03 ... (remaining 3577 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4643 2.77 - 3.30: 17789 3.30 - 3.84: 32871 3.84 - 4.37: 40174 4.37 - 4.90: 67178 Nonbonded interactions: 162655 Sorted by model distance: nonbonded pdb=" OG1 THR E 132 " pdb=" OH TYR E 218 " model vdw 2.240 3.040 nonbonded pdb=" O TYR E 190 " pdb=" OH TYR E 223 " model vdw 2.252 3.040 nonbonded pdb=" OG SER A 54 " pdb=" O PRO A 113 " model vdw 2.258 3.040 nonbonded pdb=" OE2 GLU A 793 " pdb=" OG SER A 801 " model vdw 2.273 3.040 nonbonded pdb=" OG SER A 150 " pdb=" OG1 THR A 162 " model vdw 2.283 3.040 ... (remaining 162650 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 25 and (name N or name CA or name C or name O or name CB \ )) or resid 26 through 27 or (resid 28 and (name N or name CA or name C or name \ O or name CB )) or resid 29 through 30 or (resid 31 through 32 and (name N or na \ me CA or name C or name O or name CB )) or resid 33 through 34 or (resid 35 and \ (name N or name CA or name C or name O or name CB )) or resid 36 through 54 or ( \ resid 55 and (name N or name CA or name C or name O or name CB )) or resid 56 th \ rough 60 or (resid 61 and (name N or name CA or name C or name O or name CB )) o \ r resid 62 through 69 or (resid 70 and (name N or name CA or name C or name O or \ name CB )) or resid 71 through 77 or (resid 78 and (name N or name CA or name C \ or name O or name CB )) or resid 79 through 85 or (resid 86 and (name N or name \ CA or name C or name O or name CB )) or resid 87 through 97 or (resid 98 throug \ h 99 and (name N or name CA or name C or name O or name CB )) or resid 100 throu \ gh 105 or (resid 106 and (name N or name CA or name C or name O or name CB )) or \ resid 107 through 118 or (resid 119 through 120 and (name N or name CA or name \ C or name O or name CB )) or resid 121 through 124 or (resid 125 and (name N or \ name CA or name C or name O or name CB )) or resid 126 through 135 or (resid 136 \ and (name N or name CA or name C or name O or name CB )) or resid 137 through 1 \ 43 or (resid 144 and (name N or name CA or name C or name O or name CB )) or res \ id 145 through 146 or (resid 147 and (name N or name CA or name C or name O or n \ ame CB )) or resid 148 through 187 or (resid 188 and (name N or name CA or name \ C or name O or name CB )) or resid 189 through 193 or (resid 194 through 195 and \ (name N or name CA or name C or name O or name CB )) or resid 196 through 225 o \ r (resid 226 through 227 and (name N or name CA or name C or name O or name CB ) \ ) or resid 228 through 229 or (resid 230 and (name N or name CA or name C or nam \ e O or name CB )) or resid 231 through 236 or (resid 237 through 238 and (name N \ or name CA or name C or name O or name CB )) or resid 239 through 253 or (resid \ 254 through 256 and (name N or name CA or name C or name O or name CB )) or res \ id 257 through 258 or (resid 259 and (name N or name CA or name C or name O or n \ ame CB )) or resid 260 through 261 or (resid 262 through 263 and (name N or name \ CA or name C or name O or name CB )) or resid 264 through 277 or (resid 278 thr \ ough 279 and (name N or name CA or name C or name O or name CB )) or resid 280 t \ hrough 290 or (resid 291 and (name N or name CA or name C or name O or name CB ) \ ) or resid 292 through 299 or (resid 300 and (name N or name CA or name C or nam \ e O or name CB )) or resid 301 or (resid 302 and (name N or name CA or name C or \ name O or name CB )) or resid 303 through 306 or (resid 307 and (name N or name \ CA or name C or name O or name CB )) or resid 308 through 330 or (resid 331 and \ (name N or name CA or name C or name O or name CB )) or resid 332 through 347 o \ r (resid 348 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 49 through 375 or (resid 376 and (name N or name CA or name C or name O or name \ CB )) or resid 377 through 378 or (resid 379 and (name N or name CA or name C or \ name O or name CB )) or resid 380 through 393 or (resid 394 and (name N or name \ CA or name C or name O or name CB )) or resid 395 through 397 or (resid 398 thr \ ough 400 and (name N or name CA or name C or name O or name CB )) or resid 401 t \ hrough 402 or (resid 403 through 404 and (name N or name CA or name C or name O \ or name CB )) or resid 405 through 407 or (resid 408 and (name N or name CA or n \ ame C or name O or name CB )) or resid 409 through 422 or (resid 423 and (name N \ or name CA or name C or name O or name CB )) or resid 424 through 432 or (resid \ 433 and (name N or name CA or name C or name O or name CB )) or resid 434 throu \ gh 448 or (resid 449 and (name N or name CA or name C or name O or name CB )) or \ resid 450 through 490 or (resid 491 and (name N or name CA or name C or name O \ or name CB )) or resid 492 or (resid 493 and (name N or name CA or name C or nam \ e O or name CB )) or resid 494 through 507 or (resid 508 through 510 and (name N \ or name CA or name C or name O or name CB )) or resid 511 through 515 or (resid \ 516 through 517 and (name N or name CA or name C or name O or name CB )) or res \ id 518 through 519 or (resid 520 through 521 and (name N or name CA or name C or \ name O or name CB )) or resid 522 through 533 or (resid 534 and (name N or name \ CA or name C or name O or name CB )) or resid 535 through 536 or (resid 537 thr \ ough 538 and (name N or name CA or name C or name O or name CB )) or resid 539 o \ r (resid 540 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 41 through 542 or (resid 543 and (name N or name CA or name C or name O or name \ CB )) or resid 544 through 552 or (resid 553 and (name N or name CA or name C or \ name O or name CB )) or resid 554 through 559 or (resid 560 and (name N or name \ CA or name C or name O or name CB )) or resid 561 through 567 or (resid 568 and \ (name N or name CA or name C or name O or name CB )) or resid 569 through 577 o \ r (resid 578 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 79 through 606 or (resid 607 and (name N or name CA or name C or name O or name \ CB )) or resid 608 through 620 or (resid 621 and (name N or name CA or name C or \ name O or name CB )) or resid 622 through 631 or (resid 632 through 634 and (na \ me N or name CA or name C or name O or name CB )) or resid 635 or (resid 636 and \ (name N or name CA or name C or name O or name CB )) or resid 637 through 640 o \ r (resid 641 through 642 and (name N or name CA or name C or name O or name CB ) \ ) or resid 643 through 647 or (resid 648 and (name N or name CA or name C or nam \ e O or name CB )) or resid 649 through 692 or (resid 693 through 694 and (name N \ or name CA or name C or name O or name CB )) or resid 695 through 696 or (resid \ 697 and (name N or name CA or name C or name O or name CB )) or resid 698 throu \ gh 710 or (resid 711 and (name N or name CA or name C or name O or name CB )) or \ resid 712 through 737 or (resid 738 through 739 and (name N or name CA or name \ C or name O or name CB )) or resid 740 through 745 or (resid 746 through 747 and \ (name N or name CA or name C or name O or name CB )) or resid 748 through 784 o \ r (resid 785 and (name N or name CA or name C or name O or name CB )) or resid 7 \ 86 through 789 or (resid 790 and (name N or name CA or name C or name O or name \ CB )) or resid 791 through 808 or (resid 809 and (name N or name CA or name C or \ name O or name CB )) or resid 810 through 817 or (resid 818 through 819 and (na \ me N or name CA or name C or name O or name CB )) or resid 820 through 835 or (r \ esid 836 and (name N or name CA or name C or name O or name CB )) or resid 837 t \ hrough 846 or (resid 847 through 850 and (name N or name CA or name C or name O \ or name CB )) or resid 851 through 857 or (resid 858 and (name N or name CA or n \ ame C or name O or name CB )) or resid 859 through 862 or (resid 863 through 864 \ and (name N or name CA or name C or name O or name CB )) or resid 865 through 8 \ 74 or (resid 875 through 876 and (name N or name CA or name C or name O or name \ CB )) or resid 877 through 923 or (resid 924 and (name N or name CA or name C or \ name O or name CB )) or resid 925 through 946 or (resid 947 through 948 and (na \ me N or name CA or name C or name O or name CB )) or resid 949 through 964 or (r \ esid 965 and (name N or name CA or name C or name O or name CB )) or resid 966 t \ hrough 1005)) selection = (chain 'B' and (resid 25 through 67 or (resid 68 through 70 and (name N or name \ CA or name C or name O or name CB )) or resid 71 through 159 or (resid 160 throu \ gh 161 and (name N or name CA or name C or name O or name CB )) or resid 162 thr \ ough 174 or (resid 175 through 176 and (name N or name CA or name C or name O or \ name CB )) or resid 177 through 178 or (resid 179 and (name N or name CA or nam \ e C or name O or name CB )) or resid 180 or (resid 181 and (name N or name CA or \ name C or name O or name CB )) or resid 182 through 463 or (resid 464 through 4 \ 65 and (name N or name CA or name C or name O or name CB )) or resid 466 through \ 525 or (resid 526 and (name N or name CA or name C or name O or name CB )) or r \ esid 527 through 673 or (resid 674 through 675 and (name N or name CA or name C \ or name O or name CB )) or resid 676 or (resid 677 and (name N or name CA or nam \ e C or name O or name CB )) or resid 678 through 833 or (resid 834 and (name N o \ r name CA or name C or name O or name CB )) or resid 835 through 856 or (resid 8 \ 57 through 858 and (name N or name CA or name C or name O or name CB )) or resid \ 859 through 873 or (resid 874 through 876 and (name N or name CA or name C or n \ ame O or name CB )) or resid 877 through 881 or (resid 882 through 884 and (name \ N or name CA or name C or name O or name CB )) or resid 885 through 889 or (res \ id 890 and (name N or name CA or name C or name O or name CB )) or resid 891 or \ (resid 892 through 893 and (name N or name CA or name C or name O or name CB )) \ or resid 894 through 895 or (resid 896 and (name N or name CA or name C or name \ O or name CB )) or resid 897 through 932 or (resid 933 through 934 and (name N o \ r name CA or name C or name O or name CB )) or resid 935 or (resid 936 through 9 \ 37 and (name N or name CA or name C or name O or name CB )) or resid 938 through \ 952 or (resid 953 and (name N or name CA or name C or name O or name CB )) or r \ esid 954 through 972 or (resid 973 through 974 and (name N or name CA or name C \ or name O or name CB )) or resid 975 or (resid 976 and (name N or name CA or nam \ e C or name O or name CB )) or resid 977 through 981 or (resid 982 and (name N o \ r name CA or name C or name O or name CB )) or resid 983 through 985 or (resid 9 \ 86 and (name N or name CA or name C or name O or name CB )) or resid 987 through \ 988 or (resid 989 and (name N or name CA or name C or name O or name CB )) or r \ esid 990 through 1005)) } ncs_group { reference = (chain 'D' and (resid 27 or (resid 28 and (name N or name CA or name C or name O \ or name CB )) or resid 29 through 30 or (resid 31 through 32 and (name N or nam \ e CA or name C or name O or name CB )) or resid 33 through 54 or (resid 55 and ( \ name N or name CA or name C or name O or name CB )) or resid 56 through 57 or (r \ esid 58 and (name N or name CA or name C or name O or name CB )) or resid 59 thr \ ough 60 or (resid 61 and (name N or name CA or name C or name O or name CB )) or \ resid 62 through 69 or (resid 70 and (name N or name CA or name C or name O or \ name CB )) or resid 71 through 97 or (resid 98 through 99 and (name N or name CA \ or name C or name O or name CB )) or resid 100 through 105 or (resid 106 and (n \ ame N or name CA or name C or name O or name CB )) or resid 107 through 118 or ( \ resid 119 through 120 and (name N or name CA or name C or name O or name CB )) o \ r resid 121 through 124 or (resid 125 and (name N or name CA or name C or name O \ or name CB )) or resid 126 through 135 or (resid 136 and (name N or name CA or \ name C or name O or name CB )) or resid 137 through 143 or (resid 144 and (name \ N or name CA or name C or name O or name CB )) or resid 145 through 146 or (resi \ d 147 and (name N or name CA or name C or name O or name CB )) or resid 148 thro \ ugh 187 or (resid 188 and (name N or name CA or name C or name O or name CB )) o \ r resid 189 through 193 or (resid 194 through 195 and (name N or name CA or name \ C or name O or name CB )) or resid 196 through 225 or (resid 226 through 227 an \ d (name N or name CA or name C or name O or name CB )) or resid 228 through 236 \ or (resid 237 through 238 and (name N or name CA or name C or name O or name CB \ )) or resid 239 through 253 or (resid 254 through 256 and (name N or name CA or \ name C or name O or name CB )) or resid 257 through 258 or (resid 259 and (name \ N or name CA or name C or name O or name CB )) or resid 260 through 261 or (resi \ d 262 through 263 and (name N or name CA or name C or name O or name CB )) or re \ sid 264 through 277 or (resid 278 through 279 and (name N or name CA or name C o \ r name O or name CB )) or resid 280 through 290 or (resid 291 and (name N or nam \ e CA or name C or name O or name CB )) or resid 292 through 297)) selection = (chain 'E' and (resid 27 through 67 or (resid 68 through 70 and (name N or name \ CA or name C or name O or name CB )) or resid 71 through 72 or (resid 73 and (na \ me N or name CA or name C or name O or name CB )) or resid 74 through 159 or (re \ sid 160 through 161 and (name N or name CA or name C or name O or name CB )) or \ resid 162 through 174 or (resid 175 through 176 and (name N or name CA or name C \ or name O or name CB )) or resid 177 through 178 or (resid 179 and (name N or n \ ame CA or name C or name O or name CB )) or resid 180 or (resid 181 and (name N \ or name CA or name C or name O or name CB )) or resid 182 through 297)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.990 Check model and map are aligned: 0.410 Set scattering table: 0.000 Process input model: 47.550 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.086 20839 Z= 0.546 Angle : 0.970 10.394 28323 Z= 0.539 Chirality : 0.059 0.298 3183 Planarity : 0.006 0.059 3580 Dihedral : 10.557 82.597 7160 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 0.49 % Allowed : 3.55 % Favored : 95.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.62 (0.11), residues: 2615 helix: -4.38 (0.06), residues: 1365 sheet: -2.05 (0.41), residues: 126 loop : -2.86 (0.15), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.004 TRP C 25 HIS 0.019 0.003 HIS B 786 PHE 0.049 0.004 PHE A 559 TYR 0.036 0.003 TYR A 996 ARG 0.013 0.001 ARG B 480 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5230 Ramachandran restraints generated. 2615 Oldfield, 0 Emsley, 2615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5230 Ramachandran restraints generated. 2615 Oldfield, 0 Emsley, 2615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 2398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 522 time to evaluate : 2.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 670 SER cc_start: 0.7776 (m) cc_final: 0.7574 (p) REVERT: A 865 LEU cc_start: 0.7839 (mm) cc_final: 0.7545 (tp) REVERT: C 98 ILE cc_start: 0.8195 (mp) cc_final: 0.7778 (mm) REVERT: D 214 VAL cc_start: 0.8786 (t) cc_final: 0.8559 (t) REVERT: E 34 THR cc_start: 0.7433 (p) cc_final: 0.7019 (p) REVERT: E 182 ASN cc_start: 0.8740 (m-40) cc_final: 0.8460 (m-40) REVERT: E 242 LYS cc_start: 0.6997 (ptpt) cc_final: 0.6634 (tttm) outliers start: 10 outliers final: 4 residues processed: 528 average time/residue: 1.2338 time to fit residues: 746.4230 Evaluate side-chains 266 residues out of total 2398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 262 time to evaluate : 2.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 942 PHE Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain C residue 26 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 220 optimal weight: 8.9990 chunk 197 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 chunk 67 optimal weight: 0.5980 chunk 133 optimal weight: 1.9990 chunk 105 optimal weight: 0.0010 chunk 204 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 chunk 152 optimal weight: 0.6980 chunk 237 optimal weight: 5.9990 overall best weight: 0.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN A 241 HIS A 339 HIS A 487 GLN A 609 HIS A 905 GLN A 939 GLN A 990 ASN B 332 HIS B 377 GLN B 487 GLN ** B 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 681 GLN B 702 ASN B 881 HIS ** B 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 973 ASN B 990 ASN D 58 GLN D 89 GLN D 93 ASN D 109 GLN D 115 ASN D 133 ASN D 236 GLN E 236 GLN E 297 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.116707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.084120 restraints weight = 49586.879| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 3.34 r_work: 0.3125 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 20839 Z= 0.186 Angle : 0.629 9.985 28323 Z= 0.330 Chirality : 0.043 0.175 3183 Planarity : 0.005 0.064 3580 Dihedral : 5.632 52.619 2879 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.45 % Allowed : 13.67 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.87 (0.13), residues: 2615 helix: -2.66 (0.11), residues: 1384 sheet: -1.77 (0.40), residues: 135 loop : -2.35 (0.16), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 25 HIS 0.006 0.001 HIS E 128 PHE 0.016 0.001 PHE A 91 TYR 0.018 0.001 TYR B 482 ARG 0.008 0.001 ARG D 61 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5230 Ramachandran restraints generated. 2615 Oldfield, 0 Emsley, 2615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5230 Ramachandran restraints generated. 2615 Oldfield, 0 Emsley, 2615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 297 time to evaluate : 2.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7247 (pp20) cc_final: 0.6919 (tm-30) REVERT: A 38 ARG cc_start: 0.8496 (mtt180) cc_final: 0.8285 (mtt-85) REVERT: A 156 GLU cc_start: 0.9187 (mp0) cc_final: 0.8899 (mp0) REVERT: A 398 LYS cc_start: 0.9011 (mppt) cc_final: 0.8630 (pptt) REVERT: A 578 MET cc_start: 0.5973 (ppp) cc_final: 0.5245 (pmt) REVERT: A 670 SER cc_start: 0.8248 (m) cc_final: 0.7917 (p) REVERT: A 865 LEU cc_start: 0.8852 (mm) cc_final: 0.8393 (tp) REVERT: B 327 LYS cc_start: 0.9110 (OUTLIER) cc_final: 0.8668 (mtmt) REVERT: B 631 ILE cc_start: 0.6836 (OUTLIER) cc_final: 0.6292 (mp) REVERT: B 936 MET cc_start: 0.8627 (mtp) cc_final: 0.8063 (mpt) REVERT: C 26 ASP cc_start: 0.8905 (t0) cc_final: 0.8645 (t0) REVERT: C 98 ILE cc_start: 0.8884 (mp) cc_final: 0.8678 (mm) REVERT: D 118 HIS cc_start: 0.8396 (m90) cc_final: 0.8188 (m90) REVERT: D 119 ASP cc_start: 0.9053 (m-30) cc_final: 0.8818 (t0) REVERT: D 134 TYR cc_start: 0.7137 (OUTLIER) cc_final: 0.6779 (p90) REVERT: D 187 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.6765 (tp30) REVERT: D 241 HIS cc_start: 0.6599 (m90) cc_final: 0.6273 (m90) REVERT: D 244 PHE cc_start: 0.8762 (OUTLIER) cc_final: 0.8466 (m-80) REVERT: D 254 GLU cc_start: 0.8006 (tp30) cc_final: 0.7777 (tp30) REVERT: D 258 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8725 (mp) REVERT: D 262 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7404 (mm-30) REVERT: E 45 PHE cc_start: 0.8528 (OUTLIER) cc_final: 0.7957 (m-80) REVERT: E 179 LYS cc_start: 0.7031 (mppt) cc_final: 0.6688 (mppt) REVERT: E 182 ASN cc_start: 0.9037 (m-40) cc_final: 0.8791 (m-40) REVERT: E 242 LYS cc_start: 0.6436 (ptpt) cc_final: 0.6154 (tttm) REVERT: E 275 ILE cc_start: 0.6755 (OUTLIER) cc_final: 0.6494 (pp) outliers start: 70 outliers final: 18 residues processed: 340 average time/residue: 1.1636 time to fit residues: 455.5448 Evaluate side-chains 255 residues out of total 2398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 229 time to evaluate : 2.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 839 PHE Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 327 LYS Chi-restraints excluded: chain B residue 518 GLU Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain C residue 47 CYS Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 244 PHE Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 45 PHE Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 275 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 127 optimal weight: 0.9990 chunk 169 optimal weight: 1.9990 chunk 216 optimal weight: 7.9990 chunk 154 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 160 optimal weight: 0.7980 chunk 208 optimal weight: 5.9990 chunk 178 optimal weight: 6.9990 chunk 67 optimal weight: 0.4980 chunk 97 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 ASN A 391 ASN A 797 ASN ** B 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 ASN D 58 GLN D 211 HIS E 78 ASN E 118 HIS E 128 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.114526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.081596 restraints weight = 49153.766| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 3.28 r_work: 0.3070 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20839 Z= 0.211 Angle : 0.594 13.705 28323 Z= 0.303 Chirality : 0.043 0.259 3183 Planarity : 0.004 0.059 3580 Dihedral : 4.971 36.727 2875 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.50 % Allowed : 15.93 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.14), residues: 2615 helix: -1.60 (0.13), residues: 1409 sheet: -1.49 (0.43), residues: 116 loop : -2.10 (0.16), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 25 HIS 0.004 0.001 HIS B 609 PHE 0.018 0.001 PHE E 240 TYR 0.023 0.001 TYR A 912 ARG 0.008 0.001 ARG D 61 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5230 Ramachandran restraints generated. 2615 Oldfield, 0 Emsley, 2615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5230 Ramachandran restraints generated. 2615 Oldfield, 0 Emsley, 2615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 252 time to evaluate : 2.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.8433 (mtt180) cc_final: 0.8179 (mtt-85) REVERT: A 156 GLU cc_start: 0.9246 (mp0) cc_final: 0.8994 (mp0) REVERT: A 398 LYS cc_start: 0.9032 (mppt) cc_final: 0.8621 (pptt) REVERT: A 560 GLU cc_start: 0.8209 (pp20) cc_final: 0.7958 (pp20) REVERT: A 578 MET cc_start: 0.6175 (ppp) cc_final: 0.5593 (tmm) REVERT: A 670 SER cc_start: 0.8209 (m) cc_final: 0.7904 (p) REVERT: A 865 LEU cc_start: 0.8824 (mm) cc_final: 0.8485 (tm) REVERT: B 624 GLU cc_start: 0.9196 (OUTLIER) cc_final: 0.8552 (tp30) REVERT: B 631 ILE cc_start: 0.6913 (OUTLIER) cc_final: 0.6435 (mp) REVERT: B 930 MET cc_start: 0.8952 (mtp) cc_final: 0.8745 (ptp) REVERT: B 936 MET cc_start: 0.8621 (mtp) cc_final: 0.8088 (mpt) REVERT: C 26 ASP cc_start: 0.8993 (t0) cc_final: 0.8605 (t0) REVERT: C 40 ASN cc_start: 0.8339 (t0) cc_final: 0.8103 (t160) REVERT: C 41 LYS cc_start: 0.9201 (OUTLIER) cc_final: 0.8756 (mmpt) REVERT: D 31 LYS cc_start: 0.9296 (pttm) cc_final: 0.9091 (pmtt) REVERT: D 119 ASP cc_start: 0.8958 (m-30) cc_final: 0.8711 (t0) REVERT: D 134 TYR cc_start: 0.7201 (p90) cc_final: 0.6922 (p90) REVERT: D 187 GLU cc_start: 0.6996 (OUTLIER) cc_final: 0.6420 (tp30) REVERT: D 241 HIS cc_start: 0.6441 (m90) cc_final: 0.6024 (m90) REVERT: D 244 PHE cc_start: 0.8733 (OUTLIER) cc_final: 0.8462 (m-80) REVERT: D 254 GLU cc_start: 0.8047 (tp30) cc_final: 0.7624 (tm-30) REVERT: D 258 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8801 (mt) REVERT: E 45 PHE cc_start: 0.8564 (OUTLIER) cc_final: 0.8071 (m-80) REVERT: E 178 PHE cc_start: 0.7026 (OUTLIER) cc_final: 0.6044 (t80) REVERT: E 179 LYS cc_start: 0.7014 (mppt) cc_final: 0.6452 (mmmt) REVERT: E 181 GLU cc_start: 0.8212 (pm20) cc_final: 0.8000 (pm20) REVERT: E 234 LYS cc_start: 0.7457 (mtmm) cc_final: 0.7244 (mtpm) REVERT: E 244 PHE cc_start: 0.6661 (OUTLIER) cc_final: 0.6380 (m-10) outliers start: 71 outliers final: 17 residues processed: 292 average time/residue: 1.1813 time to fit residues: 397.2144 Evaluate side-chains 251 residues out of total 2398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 225 time to evaluate : 2.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 839 PHE Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 624 GLU Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 764 CYS Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 47 CYS Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 244 PHE Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 45 PHE Chi-restraints excluded: chain E residue 178 PHE Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 244 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 56 optimal weight: 1.9990 chunk 148 optimal weight: 6.9990 chunk 140 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 206 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 162 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 163 optimal weight: 4.9990 chunk 197 optimal weight: 0.9980 chunk 166 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 797 ASN ** B 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 666 ASN ** B 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.114626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.081706 restraints weight = 50334.312| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 3.30 r_work: 0.3076 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.3733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 20839 Z= 0.180 Angle : 0.564 9.788 28323 Z= 0.287 Chirality : 0.042 0.168 3183 Planarity : 0.003 0.037 3580 Dihedral : 4.681 34.352 2875 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.16 % Allowed : 17.12 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.15), residues: 2615 helix: -0.99 (0.13), residues: 1402 sheet: -1.37 (0.41), residues: 130 loop : -1.86 (0.17), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 60 HIS 0.004 0.001 HIS A 339 PHE 0.019 0.001 PHE E 240 TYR 0.016 0.001 TYR A 912 ARG 0.009 0.001 ARG D 61 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5230 Ramachandran restraints generated. 2615 Oldfield, 0 Emsley, 2615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5230 Ramachandran restraints generated. 2615 Oldfield, 0 Emsley, 2615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 240 time to evaluate : 2.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 TYR cc_start: 0.4365 (OUTLIER) cc_final: 0.3370 (t80) REVERT: A 84 TYR cc_start: 0.8734 (t80) cc_final: 0.8301 (t80) REVERT: A 398 LYS cc_start: 0.9029 (mppt) cc_final: 0.8631 (pptt) REVERT: A 560 GLU cc_start: 0.8266 (pp20) cc_final: 0.7986 (pp20) REVERT: A 578 MET cc_start: 0.6204 (ppp) cc_final: 0.5728 (tmm) REVERT: A 670 SER cc_start: 0.8158 (m) cc_final: 0.7888 (p) REVERT: A 865 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8498 (tm) REVERT: A 913 MET cc_start: 0.8808 (OUTLIER) cc_final: 0.8508 (mtm) REVERT: B 335 GLU cc_start: 0.8927 (OUTLIER) cc_final: 0.8427 (mp0) REVERT: B 624 GLU cc_start: 0.9181 (OUTLIER) cc_final: 0.8169 (tp30) REVERT: B 631 ILE cc_start: 0.7016 (OUTLIER) cc_final: 0.6568 (mp) REVERT: B 936 MET cc_start: 0.8585 (mtp) cc_final: 0.8077 (mpt) REVERT: B 989 LYS cc_start: 0.9356 (OUTLIER) cc_final: 0.9011 (ttmm) REVERT: C 40 ASN cc_start: 0.8350 (t0) cc_final: 0.8071 (t0) REVERT: C 41 LYS cc_start: 0.9186 (OUTLIER) cc_final: 0.8984 (mptm) REVERT: C 97 GLU cc_start: 0.8675 (pm20) cc_final: 0.8344 (pp20) REVERT: D 134 TYR cc_start: 0.7234 (p90) cc_final: 0.6976 (p90) REVERT: D 241 HIS cc_start: 0.6293 (m90) cc_final: 0.5900 (m90) REVERT: D 244 PHE cc_start: 0.8709 (OUTLIER) cc_final: 0.8428 (m-80) REVERT: D 254 GLU cc_start: 0.8061 (tp30) cc_final: 0.7643 (tm-30) REVERT: D 258 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8781 (mt) REVERT: D 267 ARG cc_start: 0.7941 (pmm-80) cc_final: 0.7647 (pmm-80) REVERT: E 45 PHE cc_start: 0.8551 (OUTLIER) cc_final: 0.8225 (m-80) REVERT: E 178 PHE cc_start: 0.7114 (OUTLIER) cc_final: 0.6296 (t80) REVERT: E 179 LYS cc_start: 0.7093 (mppt) cc_final: 0.6639 (mmmt) REVERT: E 234 LYS cc_start: 0.7494 (mtmm) cc_final: 0.7271 (mtpm) REVERT: E 244 PHE cc_start: 0.6535 (OUTLIER) cc_final: 0.6236 (m-10) outliers start: 64 outliers final: 22 residues processed: 277 average time/residue: 1.2092 time to fit residues: 385.1127 Evaluate side-chains 253 residues out of total 2398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 218 time to evaluate : 2.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 TYR Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 913 MET Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 624 GLU Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain B residue 989 LYS Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 47 CYS Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 244 PHE Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 45 PHE Chi-restraints excluded: chain E residue 178 PHE Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 244 PHE Chi-restraints excluded: chain E residue 269 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 39 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 203 optimal weight: 0.0870 chunk 20 optimal weight: 2.9990 chunk 173 optimal weight: 0.9990 chunk 32 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 overall best weight: 1.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 467 ASN B 681 GLN B 852 HIS ** B 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 HIS E 160 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.112826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.077217 restraints weight = 51031.304| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 3.55 r_work: 0.3005 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20839 Z= 0.253 Angle : 0.590 9.991 28323 Z= 0.301 Chirality : 0.043 0.165 3183 Planarity : 0.003 0.039 3580 Dihedral : 4.573 27.770 2873 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.80 % Allowed : 17.37 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.16), residues: 2615 helix: -0.69 (0.14), residues: 1424 sheet: -1.55 (0.43), residues: 116 loop : -1.62 (0.17), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 60 HIS 0.004 0.001 HIS B 609 PHE 0.015 0.001 PHE E 240 TYR 0.014 0.001 TYR A 912 ARG 0.009 0.001 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5230 Ramachandran restraints generated. 2615 Oldfield, 0 Emsley, 2615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5230 Ramachandran restraints generated. 2615 Oldfield, 0 Emsley, 2615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 237 time to evaluate : 2.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 TYR cc_start: 0.4665 (OUTLIER) cc_final: 0.3389 (t80) REVERT: A 84 TYR cc_start: 0.8740 (t80) cc_final: 0.8334 (t80) REVERT: A 202 ASN cc_start: 0.9010 (m-40) cc_final: 0.8451 (t0) REVERT: A 398 LYS cc_start: 0.9032 (mppt) cc_final: 0.8641 (pptt) REVERT: A 560 GLU cc_start: 0.8365 (pp20) cc_final: 0.8110 (pp20) REVERT: A 578 MET cc_start: 0.6381 (ppp) cc_final: 0.5959 (tmm) REVERT: A 670 SER cc_start: 0.8173 (m) cc_final: 0.7851 (p) REVERT: A 865 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8541 (tm) REVERT: A 913 MET cc_start: 0.8977 (mtp) cc_final: 0.8704 (mtm) REVERT: B 335 GLU cc_start: 0.9071 (OUTLIER) cc_final: 0.8606 (mp0) REVERT: B 624 GLU cc_start: 0.9212 (OUTLIER) cc_final: 0.8084 (tp30) REVERT: B 631 ILE cc_start: 0.6966 (OUTLIER) cc_final: 0.6556 (mp) REVERT: B 936 MET cc_start: 0.8626 (mtp) cc_final: 0.8072 (mpt) REVERT: B 989 LYS cc_start: 0.9351 (OUTLIER) cc_final: 0.9060 (ttmm) REVERT: D 134 TYR cc_start: 0.7313 (p90) cc_final: 0.6979 (p90) REVERT: D 242 LYS cc_start: 0.7336 (OUTLIER) cc_final: 0.6999 (mppt) REVERT: D 244 PHE cc_start: 0.8818 (OUTLIER) cc_final: 0.8554 (m-80) REVERT: D 254 GLU cc_start: 0.8007 (tp30) cc_final: 0.7624 (tm-30) REVERT: E 45 PHE cc_start: 0.8611 (OUTLIER) cc_final: 0.8310 (m-80) REVERT: E 178 PHE cc_start: 0.7214 (OUTLIER) cc_final: 0.6453 (t80) REVERT: E 179 LYS cc_start: 0.7169 (mppt) cc_final: 0.6606 (mmmt) REVERT: E 182 ASN cc_start: 0.8904 (m-40) cc_final: 0.8660 (m110) REVERT: E 222 ASP cc_start: 0.8466 (t0) cc_final: 0.8195 (m-30) REVERT: E 242 LYS cc_start: 0.6113 (OUTLIER) cc_final: 0.5337 (tptp) REVERT: E 244 PHE cc_start: 0.6725 (OUTLIER) cc_final: 0.6444 (m-10) REVERT: E 247 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.8031 (ptm160) outliers start: 77 outliers final: 32 residues processed: 291 average time/residue: 1.1762 time to fit residues: 395.7294 Evaluate side-chains 258 residues out of total 2398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 213 time to evaluate : 2.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 79 TYR Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 839 PHE Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 349 HIS Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 531 MET Chi-restraints excluded: chain B residue 624 GLU Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 764 CYS Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain B residue 989 LYS Chi-restraints excluded: chain C residue 47 CYS Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 242 LYS Chi-restraints excluded: chain D residue 244 PHE Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 45 PHE Chi-restraints excluded: chain E residue 178 PHE Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 242 LYS Chi-restraints excluded: chain E residue 244 PHE Chi-restraints excluded: chain E residue 247 ARG Chi-restraints excluded: chain E residue 269 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 94 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 chunk 242 optimal weight: 2.9990 chunk 210 optimal weight: 10.0000 chunk 238 optimal weight: 10.0000 chunk 61 optimal weight: 0.8980 chunk 226 optimal weight: 9.9990 chunk 128 optimal weight: 0.0970 chunk 216 optimal weight: 9.9990 chunk 218 optimal weight: 9.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.113380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.077786 restraints weight = 50597.118| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 3.53 r_work: 0.3020 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.4262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 20839 Z= 0.209 Angle : 0.584 15.355 28323 Z= 0.293 Chirality : 0.043 0.182 3183 Planarity : 0.003 0.040 3580 Dihedral : 4.434 25.668 2873 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.40 % Allowed : 18.55 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.16), residues: 2615 helix: -0.32 (0.14), residues: 1408 sheet: -1.38 (0.43), residues: 118 loop : -1.41 (0.18), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 60 HIS 0.004 0.001 HIS A 339 PHE 0.015 0.001 PHE B 301 TYR 0.018 0.001 TYR D 197 ARG 0.010 0.001 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5230 Ramachandran restraints generated. 2615 Oldfield, 0 Emsley, 2615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5230 Ramachandran restraints generated. 2615 Oldfield, 0 Emsley, 2615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 225 time to evaluate : 2.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 TYR cc_start: 0.4801 (OUTLIER) cc_final: 0.3501 (t80) REVERT: A 84 TYR cc_start: 0.8738 (t80) cc_final: 0.8398 (t80) REVERT: A 202 ASN cc_start: 0.8981 (m-40) cc_final: 0.8432 (t0) REVERT: A 398 LYS cc_start: 0.9045 (mppt) cc_final: 0.8653 (pptt) REVERT: A 560 GLU cc_start: 0.8326 (pp20) cc_final: 0.8068 (pp20) REVERT: A 578 MET cc_start: 0.6440 (ppp) cc_final: 0.5857 (tmm) REVERT: A 670 SER cc_start: 0.8142 (m) cc_final: 0.7839 (p) REVERT: A 865 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8515 (tm) REVERT: A 913 MET cc_start: 0.8976 (mtp) cc_final: 0.8679 (mtm) REVERT: B 335 GLU cc_start: 0.9054 (OUTLIER) cc_final: 0.8572 (mp0) REVERT: B 631 ILE cc_start: 0.7009 (OUTLIER) cc_final: 0.6603 (mp) REVERT: B 913 MET cc_start: 0.8637 (tpt) cc_final: 0.8407 (tpt) REVERT: B 936 MET cc_start: 0.8620 (mtp) cc_final: 0.8107 (mpt) REVERT: B 989 LYS cc_start: 0.9356 (OUTLIER) cc_final: 0.9061 (ttpp) REVERT: C 58 ASP cc_start: 0.7506 (m-30) cc_final: 0.6947 (p0) REVERT: C 97 GLU cc_start: 0.8713 (pm20) cc_final: 0.8415 (pp20) REVERT: D 148 TYR cc_start: 0.8337 (t80) cc_final: 0.7795 (t80) REVERT: D 244 PHE cc_start: 0.8743 (OUTLIER) cc_final: 0.8486 (m-80) REVERT: D 253 ILE cc_start: 0.8471 (tp) cc_final: 0.8271 (mt) REVERT: D 254 GLU cc_start: 0.8014 (tp30) cc_final: 0.7397 (tm-30) REVERT: D 256 GLU cc_start: 0.7475 (mp0) cc_final: 0.6885 (mp0) REVERT: D 258 LEU cc_start: 0.9037 (tm) cc_final: 0.8761 (mt) REVERT: D 278 ASN cc_start: 0.8629 (m110) cc_final: 0.8409 (p0) REVERT: E 178 PHE cc_start: 0.7231 (OUTLIER) cc_final: 0.6456 (t80) REVERT: E 179 LYS cc_start: 0.7203 (mppt) cc_final: 0.6052 (mmmt) REVERT: E 181 GLU cc_start: 0.7894 (pm20) cc_final: 0.7579 (pm20) REVERT: E 208 ILE cc_start: 0.8534 (mt) cc_final: 0.8313 (mp) REVERT: E 222 ASP cc_start: 0.8445 (t0) cc_final: 0.8200 (m-30) REVERT: E 242 LYS cc_start: 0.6137 (ttpp) cc_final: 0.5450 (tptp) REVERT: E 244 PHE cc_start: 0.6691 (OUTLIER) cc_final: 0.6401 (m-10) outliers start: 69 outliers final: 38 residues processed: 273 average time/residue: 1.1353 time to fit residues: 358.6541 Evaluate side-chains 261 residues out of total 2398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 215 time to evaluate : 2.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 TYR Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 827 LEU Chi-restraints excluded: chain A residue 839 PHE Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 914 SER Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 143 TRP Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 349 HIS Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 764 CYS Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain B residue 878 THR Chi-restraints excluded: chain B residue 989 LYS Chi-restraints excluded: chain B residue 1005 ILE Chi-restraints excluded: chain C residue 47 CYS Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 244 PHE Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 178 PHE Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 244 PHE Chi-restraints excluded: chain E residue 269 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 209 optimal weight: 2.9990 chunk 127 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 72 optimal weight: 0.0970 chunk 19 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 254 optimal weight: 6.9990 chunk 141 optimal weight: 0.0870 chunk 195 optimal weight: 4.9990 overall best weight: 0.5556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 939 GLN ** B 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 HIS C 40 ASN E 128 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.114168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.080182 restraints weight = 50075.583| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 3.38 r_work: 0.3074 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.4488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 20839 Z= 0.147 Angle : 0.571 16.654 28323 Z= 0.283 Chirality : 0.041 0.152 3183 Planarity : 0.003 0.036 3580 Dihedral : 4.255 26.629 2873 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.52 % Allowed : 20.18 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.16), residues: 2615 helix: 0.00 (0.14), residues: 1394 sheet: -1.31 (0.43), residues: 118 loop : -1.19 (0.18), residues: 1103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 60 HIS 0.004 0.001 HIS A 339 PHE 0.015 0.001 PHE E 240 TYR 0.016 0.001 TYR D 197 ARG 0.007 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5230 Ramachandran restraints generated. 2615 Oldfield, 0 Emsley, 2615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5230 Ramachandran restraints generated. 2615 Oldfield, 0 Emsley, 2615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 234 time to evaluate : 2.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.8446 (mtt-85) cc_final: 0.8055 (mmt-90) REVERT: A 79 TYR cc_start: 0.4715 (OUTLIER) cc_final: 0.3474 (t80) REVERT: A 84 TYR cc_start: 0.8751 (t80) cc_final: 0.8452 (t80) REVERT: A 202 ASN cc_start: 0.8952 (m-40) cc_final: 0.8395 (t0) REVERT: A 398 LYS cc_start: 0.9026 (mppt) cc_final: 0.8647 (pptt) REVERT: A 560 GLU cc_start: 0.8237 (pp20) cc_final: 0.7926 (pp20) REVERT: A 569 MET cc_start: 0.6911 (tpt) cc_final: 0.6588 (tpt) REVERT: A 578 MET cc_start: 0.6421 (ppp) cc_final: 0.5850 (tmm) REVERT: A 670 SER cc_start: 0.8085 (m) cc_final: 0.7856 (p) REVERT: A 865 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8511 (tm) REVERT: A 913 MET cc_start: 0.8892 (mtp) cc_final: 0.8605 (mtm) REVERT: B 335 GLU cc_start: 0.8992 (OUTLIER) cc_final: 0.8504 (mp0) REVERT: B 631 ILE cc_start: 0.7058 (OUTLIER) cc_final: 0.6654 (mp) REVERT: B 936 MET cc_start: 0.8535 (mtp) cc_final: 0.8105 (mpt) REVERT: B 989 LYS cc_start: 0.9325 (OUTLIER) cc_final: 0.9058 (ttpp) REVERT: C 40 ASN cc_start: 0.8303 (t0) cc_final: 0.7523 (t0) REVERT: C 41 LYS cc_start: 0.9114 (mmtp) cc_final: 0.8556 (mmpt) REVERT: C 58 ASP cc_start: 0.7467 (m-30) cc_final: 0.6833 (p0) REVERT: C 97 GLU cc_start: 0.8699 (pm20) cc_final: 0.8425 (pp20) REVERT: D 119 ASP cc_start: 0.8486 (t0) cc_final: 0.8242 (t0) REVERT: D 148 TYR cc_start: 0.8389 (t80) cc_final: 0.7848 (t80) REVERT: D 244 PHE cc_start: 0.8753 (OUTLIER) cc_final: 0.8534 (m-80) REVERT: D 254 GLU cc_start: 0.8034 (tp30) cc_final: 0.7572 (tm-30) REVERT: D 256 GLU cc_start: 0.7539 (mp0) cc_final: 0.6877 (mp0) REVERT: D 258 LEU cc_start: 0.9059 (tm) cc_final: 0.8745 (mp) REVERT: E 89 GLN cc_start: 0.7479 (mp10) cc_final: 0.7176 (tp-100) REVERT: E 143 TRP cc_start: 0.8709 (t60) cc_final: 0.8212 (t-100) REVERT: E 178 PHE cc_start: 0.7132 (OUTLIER) cc_final: 0.6555 (t80) REVERT: E 179 LYS cc_start: 0.6417 (mppt) cc_final: 0.5904 (mmmt) REVERT: E 181 GLU cc_start: 0.7590 (pm20) cc_final: 0.7383 (pp20) REVERT: E 187 GLU cc_start: 0.7092 (tp30) cc_final: 0.6549 (pm20) REVERT: E 222 ASP cc_start: 0.8455 (t0) cc_final: 0.8197 (m-30) REVERT: E 242 LYS cc_start: 0.6178 (ttpp) cc_final: 0.5503 (tptp) REVERT: E 244 PHE cc_start: 0.6468 (OUTLIER) cc_final: 0.6217 (m-10) REVERT: E 247 ARG cc_start: 0.8511 (ptm160) cc_final: 0.8298 (ptm160) outliers start: 51 outliers final: 27 residues processed: 268 average time/residue: 1.1753 time to fit residues: 364.0120 Evaluate side-chains 249 residues out of total 2398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 214 time to evaluate : 2.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 TYR Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 827 LEU Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 143 TRP Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 349 HIS Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 764 CYS Chi-restraints excluded: chain B residue 878 THR Chi-restraints excluded: chain B residue 989 LYS Chi-restraints excluded: chain B residue 1005 ILE Chi-restraints excluded: chain C residue 47 CYS Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 244 PHE Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 178 PHE Chi-restraints excluded: chain E residue 244 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 162 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 182 optimal weight: 5.9990 chunk 161 optimal weight: 1.9990 chunk 14 optimal weight: 8.9990 chunk 9 optimal weight: 0.3980 chunk 194 optimal weight: 0.9990 chunk 125 optimal weight: 6.9990 chunk 128 optimal weight: 0.4980 chunk 74 optimal weight: 0.6980 chunk 147 optimal weight: 0.8980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 990 ASN D 93 ASN E 128 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.114550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.080445 restraints weight = 49862.592| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 3.74 r_work: 0.3014 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.4640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 20839 Z= 0.155 Angle : 0.576 14.131 28323 Z= 0.285 Chirality : 0.041 0.151 3183 Planarity : 0.003 0.035 3580 Dihedral : 4.152 25.931 2873 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.52 % Allowed : 20.92 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.17), residues: 2615 helix: 0.25 (0.15), residues: 1386 sheet: -1.19 (0.44), residues: 112 loop : -1.07 (0.18), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 60 HIS 0.004 0.001 HIS A 339 PHE 0.017 0.001 PHE E 240 TYR 0.014 0.001 TYR D 197 ARG 0.006 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5230 Ramachandran restraints generated. 2615 Oldfield, 0 Emsley, 2615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5230 Ramachandran restraints generated. 2615 Oldfield, 0 Emsley, 2615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 222 time to evaluate : 2.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.8339 (mtt-85) cc_final: 0.7937 (mmt-90) REVERT: A 79 TYR cc_start: 0.4684 (OUTLIER) cc_final: 0.3500 (t80) REVERT: A 84 TYR cc_start: 0.8796 (t80) cc_final: 0.8512 (t80) REVERT: A 202 ASN cc_start: 0.8939 (m-40) cc_final: 0.8378 (t0) REVERT: A 560 GLU cc_start: 0.8283 (pp20) cc_final: 0.7993 (pp20) REVERT: A 569 MET cc_start: 0.6903 (tpt) cc_final: 0.6635 (tpt) REVERT: A 578 MET cc_start: 0.6456 (ppp) cc_final: 0.5886 (tmm) REVERT: A 670 SER cc_start: 0.8037 (m) cc_final: 0.7823 (p) REVERT: A 913 MET cc_start: 0.8959 (mtp) cc_final: 0.8701 (mtm) REVERT: B 107 PHE cc_start: 0.7764 (OUTLIER) cc_final: 0.7523 (t80) REVERT: B 335 GLU cc_start: 0.8995 (OUTLIER) cc_final: 0.8514 (mp0) REVERT: B 631 ILE cc_start: 0.6943 (OUTLIER) cc_final: 0.6567 (mp) REVERT: B 913 MET cc_start: 0.8553 (tpt) cc_final: 0.8347 (tpt) REVERT: B 936 MET cc_start: 0.8578 (mtp) cc_final: 0.8113 (mpt) REVERT: B 989 LYS cc_start: 0.9293 (OUTLIER) cc_final: 0.8987 (ttpp) REVERT: C 97 GLU cc_start: 0.8815 (pm20) cc_final: 0.8542 (pp20) REVERT: D 61 ARG cc_start: 0.8953 (mtm110) cc_final: 0.8187 (ttp-170) REVERT: D 119 ASP cc_start: 0.8530 (t0) cc_final: 0.8254 (t0) REVERT: D 148 TYR cc_start: 0.8360 (t80) cc_final: 0.7817 (t80) REVERT: D 253 ILE cc_start: 0.8427 (tp) cc_final: 0.8099 (mt) REVERT: D 254 GLU cc_start: 0.7960 (tp30) cc_final: 0.7326 (tm-30) REVERT: D 256 GLU cc_start: 0.7501 (mp0) cc_final: 0.6907 (mp0) REVERT: D 258 LEU cc_start: 0.9055 (tm) cc_final: 0.8793 (mt) REVERT: E 143 TRP cc_start: 0.8740 (t60) cc_final: 0.8238 (t-100) REVERT: E 178 PHE cc_start: 0.7222 (OUTLIER) cc_final: 0.6677 (t80) REVERT: E 179 LYS cc_start: 0.6380 (mppt) cc_final: 0.5886 (mmmt) REVERT: E 181 GLU cc_start: 0.7619 (pm20) cc_final: 0.7267 (pp20) REVERT: E 222 ASP cc_start: 0.8395 (t0) cc_final: 0.8139 (m-30) REVERT: E 242 LYS cc_start: 0.6047 (ttpp) cc_final: 0.5672 (mtpt) REVERT: E 244 PHE cc_start: 0.6553 (OUTLIER) cc_final: 0.6289 (m-10) REVERT: E 247 ARG cc_start: 0.8516 (ptm160) cc_final: 0.8003 (ppp80) outliers start: 51 outliers final: 29 residues processed: 255 average time/residue: 1.1428 time to fit residues: 336.2475 Evaluate side-chains 251 residues out of total 2398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 215 time to evaluate : 2.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 TYR Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 839 PHE Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 107 PHE Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 143 TRP Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 349 HIS Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 764 CYS Chi-restraints excluded: chain B residue 878 THR Chi-restraints excluded: chain B residue 989 LYS Chi-restraints excluded: chain C residue 47 CYS Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 64 ASP Chi-restraints excluded: chain E residue 178 PHE Chi-restraints excluded: chain E residue 244 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 110 optimal weight: 6.9990 chunk 195 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 116 optimal weight: 0.8980 chunk 134 optimal weight: 2.9990 chunk 26 optimal weight: 8.9990 chunk 223 optimal weight: 5.9990 chunk 52 optimal weight: 0.0270 chunk 24 optimal weight: 0.8980 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 905 GLN ** B 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 HIS ** E 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.114733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.080474 restraints weight = 49961.954| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 3.78 r_work: 0.3021 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.4733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 20839 Z= 0.153 Angle : 0.584 13.650 28323 Z= 0.286 Chirality : 0.041 0.165 3183 Planarity : 0.003 0.036 3580 Dihedral : 4.099 25.940 2873 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.61 % Allowed : 20.92 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.17), residues: 2615 helix: 0.36 (0.15), residues: 1382 sheet: -1.09 (0.44), residues: 112 loop : -0.97 (0.18), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP A 60 HIS 0.003 0.001 HIS A 339 PHE 0.017 0.001 PHE E 240 TYR 0.016 0.001 TYR A 552 ARG 0.006 0.000 ARG D 165 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5230 Ramachandran restraints generated. 2615 Oldfield, 0 Emsley, 2615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5230 Ramachandran restraints generated. 2615 Oldfield, 0 Emsley, 2615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 224 time to evaluate : 2.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.8329 (mtt-85) cc_final: 0.8003 (mmt-90) REVERT: A 79 TYR cc_start: 0.4613 (OUTLIER) cc_final: 0.3494 (t80) REVERT: A 84 TYR cc_start: 0.8857 (t80) cc_final: 0.8500 (t80) REVERT: A 202 ASN cc_start: 0.8931 (m-40) cc_final: 0.8372 (t0) REVERT: A 560 GLU cc_start: 0.8270 (pp20) cc_final: 0.7980 (pp20) REVERT: A 569 MET cc_start: 0.6937 (tpt) cc_final: 0.6667 (tpt) REVERT: A 578 MET cc_start: 0.6495 (ppp) cc_final: 0.5935 (tmm) REVERT: A 865 LEU cc_start: 0.8825 (mm) cc_final: 0.8539 (tm) REVERT: A 913 MET cc_start: 0.8941 (mtp) cc_final: 0.8715 (mtm) REVERT: B 335 GLU cc_start: 0.8982 (OUTLIER) cc_final: 0.8500 (mp0) REVERT: B 631 ILE cc_start: 0.6976 (OUTLIER) cc_final: 0.6599 (mp) REVERT: B 936 MET cc_start: 0.8559 (mtp) cc_final: 0.8121 (mpt) REVERT: B 989 LYS cc_start: 0.9275 (OUTLIER) cc_final: 0.8970 (ttpp) REVERT: D 119 ASP cc_start: 0.8523 (t0) cc_final: 0.8226 (t0) REVERT: D 148 TYR cc_start: 0.8435 (t80) cc_final: 0.7848 (t80) REVERT: D 247 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.7554 (tmt90) REVERT: D 254 GLU cc_start: 0.7935 (tp30) cc_final: 0.7369 (tm-30) REVERT: D 256 GLU cc_start: 0.7526 (mp0) cc_final: 0.6985 (mp0) REVERT: D 258 LEU cc_start: 0.9066 (tm) cc_final: 0.8774 (mt) REVERT: D 267 ARG cc_start: 0.7805 (pmm-80) cc_final: 0.7595 (pmm-80) REVERT: E 143 TRP cc_start: 0.8730 (t60) cc_final: 0.8263 (t-100) REVERT: E 178 PHE cc_start: 0.7146 (OUTLIER) cc_final: 0.6688 (t80) REVERT: E 179 LYS cc_start: 0.6393 (mppt) cc_final: 0.6173 (mmmt) REVERT: E 187 GLU cc_start: 0.7031 (tp30) cc_final: 0.6510 (pm20) REVERT: E 222 ASP cc_start: 0.8408 (t0) cc_final: 0.8049 (t70) REVERT: E 247 ARG cc_start: 0.8527 (ptm160) cc_final: 0.8082 (ppp80) outliers start: 53 outliers final: 30 residues processed: 262 average time/residue: 1.2264 time to fit residues: 370.7656 Evaluate side-chains 244 residues out of total 2398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 208 time to evaluate : 2.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 TYR Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 839 PHE Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 143 TRP Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 349 HIS Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 824 THR Chi-restraints excluded: chain B residue 878 THR Chi-restraints excluded: chain B residue 989 LYS Chi-restraints excluded: chain C residue 47 CYS Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 64 ASP Chi-restraints excluded: chain E residue 178 PHE Chi-restraints excluded: chain E residue 269 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 8 optimal weight: 0.0570 chunk 24 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 242 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 229 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 12 optimal weight: 0.5980 chunk 224 optimal weight: 5.9990 chunk 202 optimal weight: 2.9990 chunk 220 optimal weight: 5.9990 overall best weight: 1.9304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 GLN B 109 GLN ** B 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 ASN E 128 HIS ** E 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.112652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.076854 restraints weight = 50557.559| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 3.46 r_work: 0.2979 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.4722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20839 Z= 0.268 Angle : 0.637 13.846 28323 Z= 0.319 Chirality : 0.044 0.216 3183 Planarity : 0.003 0.036 3580 Dihedral : 4.261 24.459 2873 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.17 % Allowed : 21.61 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.17), residues: 2615 helix: 0.28 (0.14), residues: 1392 sheet: -0.62 (0.53), residues: 78 loop : -0.96 (0.18), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.003 TRP D 231 HIS 0.004 0.001 HIS A 118 PHE 0.023 0.001 PHE B 107 TYR 0.017 0.001 TYR D 286 ARG 0.006 0.001 ARG A 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5230 Ramachandran restraints generated. 2615 Oldfield, 0 Emsley, 2615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5230 Ramachandran restraints generated. 2615 Oldfield, 0 Emsley, 2615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 217 time to evaluate : 2.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.8447 (mtt-85) cc_final: 0.8061 (mmt-90) REVERT: A 79 TYR cc_start: 0.5035 (OUTLIER) cc_final: 0.3461 (t80) REVERT: A 202 ASN cc_start: 0.8977 (m-40) cc_final: 0.8411 (t0) REVERT: A 398 LYS cc_start: 0.9049 (mppt) cc_final: 0.8695 (pptt) REVERT: A 560 GLU cc_start: 0.8327 (pp20) cc_final: 0.7996 (pp20) REVERT: A 569 MET cc_start: 0.6975 (tpt) cc_final: 0.6678 (tpt) REVERT: A 578 MET cc_start: 0.6567 (ppp) cc_final: 0.6020 (tmm) REVERT: A 865 LEU cc_start: 0.8856 (mm) cc_final: 0.8540 (tm) REVERT: B 335 GLU cc_start: 0.9051 (OUTLIER) cc_final: 0.8560 (mp0) REVERT: B 631 ILE cc_start: 0.6951 (OUTLIER) cc_final: 0.6572 (mp) REVERT: B 936 MET cc_start: 0.8609 (mtp) cc_final: 0.8150 (mpt) REVERT: B 989 LYS cc_start: 0.9317 (OUTLIER) cc_final: 0.9034 (ttpp) REVERT: C 40 ASN cc_start: 0.8355 (t0) cc_final: 0.7987 (t0) REVERT: C 41 LYS cc_start: 0.9108 (mmtp) cc_final: 0.8562 (mmpt) REVERT: C 97 GLU cc_start: 0.8657 (pm20) cc_final: 0.8390 (pp20) REVERT: D 119 ASP cc_start: 0.8545 (t0) cc_final: 0.8246 (t0) REVERT: D 247 ARG cc_start: 0.7792 (OUTLIER) cc_final: 0.7497 (tmt90) REVERT: D 254 GLU cc_start: 0.7970 (tp30) cc_final: 0.7400 (tp30) REVERT: D 256 GLU cc_start: 0.7544 (mp0) cc_final: 0.7086 (mp0) REVERT: D 258 LEU cc_start: 0.9049 (tm) cc_final: 0.8726 (mt) REVERT: E 89 GLN cc_start: 0.8914 (tp-100) cc_final: 0.8387 (mp10) REVERT: E 143 TRP cc_start: 0.8725 (t60) cc_final: 0.8303 (t-100) REVERT: E 178 PHE cc_start: 0.7242 (OUTLIER) cc_final: 0.7001 (t80) REVERT: E 179 LYS cc_start: 0.6415 (mppt) cc_final: 0.5956 (mmmt) REVERT: E 181 GLU cc_start: 0.7843 (pm20) cc_final: 0.7343 (pp20) REVERT: E 222 ASP cc_start: 0.8451 (t0) cc_final: 0.8074 (t70) REVERT: E 242 LYS cc_start: 0.5866 (mtpp) cc_final: 0.5148 (tppp) REVERT: E 244 PHE cc_start: 0.6670 (OUTLIER) cc_final: 0.6395 (m-10) REVERT: E 247 ARG cc_start: 0.8578 (ptm160) cc_final: 0.8100 (ppp80) outliers start: 44 outliers final: 32 residues processed: 250 average time/residue: 1.2176 time to fit residues: 349.4670 Evaluate side-chains 238 residues out of total 2398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 199 time to evaluate : 2.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 TYR Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 839 PHE Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 143 TRP Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 349 HIS Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 764 CYS Chi-restraints excluded: chain B residue 824 THR Chi-restraints excluded: chain B residue 878 THR Chi-restraints excluded: chain B residue 989 LYS Chi-restraints excluded: chain C residue 47 CYS Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 64 ASP Chi-restraints excluded: chain E residue 178 PHE Chi-restraints excluded: chain E residue 244 PHE Chi-restraints excluded: chain E residue 269 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 260 optimal weight: 5.9990 chunk 114 optimal weight: 0.2980 chunk 19 optimal weight: 3.9990 chunk 258 optimal weight: 20.0000 chunk 162 optimal weight: 0.8980 chunk 157 optimal weight: 0.9980 chunk 243 optimal weight: 0.0980 chunk 123 optimal weight: 4.9990 chunk 250 optimal weight: 7.9990 chunk 91 optimal weight: 7.9990 chunk 33 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 GLN B 160 ASN ** B 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.113985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.079539 restraints weight = 50047.843| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 3.39 r_work: 0.3061 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.4875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 20839 Z= 0.161 Angle : 0.622 14.581 28323 Z= 0.305 Chirality : 0.042 0.157 3183 Planarity : 0.003 0.056 3580 Dihedral : 4.166 26.111 2873 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.83 % Allowed : 22.15 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.17), residues: 2615 helix: 0.43 (0.15), residues: 1387 sheet: -0.71 (0.51), residues: 90 loop : -0.88 (0.19), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP A 60 HIS 0.003 0.001 HIS A 118 PHE 0.039 0.001 PHE B 107 TYR 0.016 0.001 TYR D 286 ARG 0.015 0.001 ARG D 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13762.06 seconds wall clock time: 244 minutes 28.99 seconds (14668.99 seconds total)